PDBsum entry: 1v9l

Oxidoreductase

PDB id: 1v9l

Contents

Protein chains

(+ 0 more) 418 a.a. *

Ligands

NAD ×6

Waters ×130

* Residue conservation analysis

PDB id:

1v9l

Name:

Oxidoreductase

Title:

L-glutamate dehydrogenase from pyrobaculum islandicum complexed with NAD

Structure:

Glutamate dehydrogenase. Chain: a, b, c, d, e, f. Synonym: hyperthermostable NAD-dependent l-glutamate dehydrogenase. Engineered: yes

Source:

Pyrobaculum islandicum. Organism_taxid: 2277. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PQS)

Resolution:

2.80Å R-factor: 0.200 R-free: 0.260

Authors:

M.W.Bhuiya,H.Sakuraba,T.Ohshima,T.Imagawa,N.Katunuma,H.Tsuge

Key ref:

M.W.Bhuiya et al. (2005). The first crystal structure of hyperthermostable NAD-dependent glutamate dehydrogenase from Pyrobaculum islandicum. J Mol Biol, 345, 325-337. PubMed id: 15571725 DOI: 10.1016/j.jmb.2004.10.063

Date:

26-Jan-04 Release date: 14-Dec-04

Protein chains

Q9Y8I4  (Q9Y8I4_PYRIS) -  Glutamate dehydrogenase

Seq: 421 a.a.

Struc: 418 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (4 terms)

DOI no: 10.1016/j.jmb.2004.10.063

J Mol Biol 345:325-337 (2005)

PubMed id: 15571725

The first crystal structure of hyperthermostable NAD-dependent glutamate dehydrogenase from Pyrobaculum islandicum.

M.W.Bhuiya, H.Sakuraba, T.Ohshima, T.Imagawa, N.Katunuma, H.Tsuge.

ABSTRACT

The extremely thermostable NAD-dependent glutamate dehydrogenase (NAD-GluDH) from Pyrobaculum islandicum, a member of the Crenarchaeota, was crystallized, and its 3D structure has been determined by X-ray diffraction methods. The homohexameric structure of Pb. islandicum glutamate dehydrogenase (Pis-GluDH) was solved and refined at a resolution of 2.9A with a crystallographic R-factor of 19.9% (Rfree 26.0%). The structure indicates that each subunit consists of two domains separated by a deep cleft containing an active site. The secondary structural elements and catalytically important residues of the enzyme were highly conserved among the NAD(P)-dependent GluDHs from other sources. A structural comparison of Pis-GluDH with other NAD(P)-dependent GluDHs suggests that a significant difference in the alpha8-loop-alpha9 region of this enzyme is associated with its coenzyme specificity. From the analysis of the 3D structure, hydrophobic interactions between intersubunits were found to be important features for the enzyme oligomerization. It has been reported that Pis-GluDH is highly thermostable, like the GluDH of the hyperthermophilic archaeum Pyrococcus furiosus, and the increase in the intersubunit ion pair networks is responsible for the extreme thermostability of the Pc. furiosus enzyme. However, the number of intersubunit ion pairs in the Pis-GluDH molecules is much smaller than those of the Pc. furiosus GluDH. The number of hydrophobic interactions at the intersubunit interfaces were increased and responsible for the extremely high thermostability. This indicates that the major molecular strategy for high thermostability of the GluDHs may be different for each hyperthermophile.

Selected figure(s)

Figure 2.
Figure 2. (a) The Pb. islandicum GluDH hexamer in a crystallographic asymmetric unit and (b) the hexameric model viewed down the threefold axis. The Figures were prepared using Pymol (http://pymol.sourceforge.net/). The A, B, C, D, E and F molecules are shown in yellow, grey, cyan, green, blue and orange, respectively.

Figure 6.
Figure 6. The largest ion pair network of seven residues in Pb. islandicum GluDH. The network is situated in a cleft of the subunits and involves E121, R125, R129, D158, E159, K162 and R418. The Figure was prepared using Pymol (http://pymol.sourceforge.net/).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 345, 325-337) copyright 2005.

Figures were selected by an automated process.